scholarly journals Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Chloe Strauss ◽  
Hongan Long ◽  
Caitlyn E. Patterson ◽  
Ronald Te ◽  
Michael Lynch
Keyword(s):  
Coral Reef ◽  
Mutation Rate ◽  
Ph Dependence ◽  
Bacterial Genome ◽  
Mutation Spectrum ◽  
Ph Change ◽  
Evolutionary Forces ◽  
Marine Habitats ◽  
Genome Wide ◽  
Evolutionary Features

ABSTRACT Recent application of mutation accumulation techniques combined with whole-genome sequencing (MA/WGS) has greatly promoted studies of spontaneous mutation. However, such explorations have rarely been conducted on marine organisms, and it is unclear how marine habitats have influenced genome stability. This report resolves the mutation rate and spectrum of the coral reef pathogen Vibrio shilonii, which causes coral bleaching and endangers the biodiversity maintained by coral reefs. We found that its mutation rate and spectrum are highly similar to those of other studied bacteria from various habitats, despite the saline environment. The mutational properties of this marine bacterium are thus controlled by other general evolutionary forces such as natural selection and genetic drift. We also found that as pH drops, the mutation rate decreases and the mutation spectrum is biased in the direction of generating G/C nucleotides. This implies that evolutionary features of this organism and perhaps other marine microbes might be altered by the increasingly acidic ocean water caused by excess CO2 emission. Nonetheless, further exploration is needed as the pH range tested in this study was rather narrow and many other possible mutation determinants, such as carbonate increase, are associated with ocean acidification. IMPORTANCE This study explored the pH dependence of a bacterial genome-wide mutation rate. We discovered that the genome-wide rates of appearance of most mutation types decrease linearly and that the mutation spectrum is biased in generating more G/C nucleotides with pH drop in the coral reef pathogen V. shilonii. This study explored the pH dependence of a bacterial genome-wide mutation rate. We discovered that the genome-wide rates of appearance of most mutation types decrease linearly and that the mutation spectrum is biased in generating more G/C nucleotides with pH drop in the coral reef pathogen V. shilonii.

scholarly journals Genome-wide identification of the GATA transcription factor family and their expression patterns under temperature and salt stress in Aspergillus oryzae

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunmiao Jiang ◽  
Gongbo Lv ◽  
Jinxin Ge ◽  
Bin He ◽  
Zhe Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Gata Transcription Factor ◽  
Starting Point ◽  
Evolutionary Features ◽  
First Time

AbstractGATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X2-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.

Effect of Acute Exposure to Ammonia on Glutamate Transport in Glial Cells Isolated From the Salamander Retina

2001 ◽  
Vol 86 (2) ◽  
pp. 836-844 ◽  
Author(s):  
Dominic Mort ◽  
Païkan Marcaggi ◽  
James Grant ◽  
David Attwell
Keyword(s):  
Glial Cells ◽  
Glutamate Uptake ◽  
Ph Dependence ◽  
Glutamate Transporter ◽  
Ammonia Concentration ◽  
Ammonia Level ◽  
Glutamate Transport ◽  
Acute Exposure ◽  
Ph Change ◽  
Glutamine Synthesis

A rise of brain ammonia level, as occurs in liver failure, initially increases glutamate accumulation in neurons and glial cells. We investigated the effect of acute exposure to ammonia on glutamate transporter currents in whole cell clamped glial cells from the salamander retina. Ammonia potentiated the current evoked by a saturating concentration ofl-glutamate, and decreased the apparent affinity of the transporter for glutamate. The potentiation had a Michaelis-Menten dependence on ammonia concentration, with a K m of 1.4 mM and a maximum potentiation of 31%. Ammonia also potentiated the transporter current produced by d-aspartate. Potentiation of the glutamate transport current was seen even with glutamine synthetase inhibited, so ammonia does not act by speeding glutamine synthesis, contrary to a suggestion in the literature. The potentiation was unchanged in the absence of Cl− ions, showing that it is not an effect on the anion current gated by the glutamate transporter. Ammonium ions were unable to substitute for Na+in driving glutamate transport. Although they can partially substitute for K+ at the cation counter-transport site of the transporter, their occupancy of these sites would produce a potentiation of <1%. Ammonium, and the weak bases methylamine and trimethylamine, increased the intracellular pH by similar amounts, and intracellular alkalinization is known to increase glutamate uptake. Methylamine and trimethylamine potentiated the uptake current by the amount expected from the known pH dependence of uptake, but ammonia gave a potentiation that was larger than could be explained by the pH change, and some potentiation of uptake by ammonia was still seen when the internal pH was 8.8, at which pH further alkalinization does not increase uptake. These data suggest that ammonia speeds glutamate uptake both by increasing cytoplasmic pH and by a separate effect on the glutamate transporter. Approximately two-thirds of the speeding is due to the pH change.

scholarly journals Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria

2017 ◽  
Author(s):  
Antoine Frénoy ◽  
Sebastian Bonhoeffer
Keyword(s):  
Population Dynamics ◽  
Mutation Rate ◽  
Death Rate ◽  
Mutation Rates ◽  
Resistance Mutations ◽  
Bacterial Populations ◽  
Plasmid Segregation ◽  
Genome Wide ◽  
Response To Stress ◽  
Induced Mutagenesis

AbstractThe stress-induced mutagenesis paradigm postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to withstand the stress. This has implications for antibiotic treatment: exposure to sub-inhibitory doses of antibiotics has been reported to increase bacterial mutation rates, and thus probably the rate at which resistance mutations appear and lead to treatment failure.Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet sub-inhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus giving more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress.We developed a system using plasmid segregation to measure death and growth rates simultaneously in bacterial populations. We use it to replicate classical experiments reporting antibiotic-induced mutagenesis. We found that a substantial death rate occurs at the tested sub-inhibitory concentrations, and taking this death into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover even when antibiotics increase mutation rate, sub-inhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics.Beside showing that population dynamic is a crucial but neglected parameter affecting evolvability, we provide better experimental and computational tools to study evolvability under stress, leading to a re-assessment of the magnitude and significance of the stress-induced mutagenesis paradigm.

scholarly journals Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shulin Zhang ◽  
Zailong Tian ◽  
Haipeng Li ◽  
Yutao Guo ◽  
Yanqi Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Plant Species ◽  
26S Proteasome ◽  
Genome Wide Analysis ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome ◽  
F Box Protein

Abstract Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.

scholarly journals Estimating the Genome-wide Mutation Rate with Three-Way Identity by Descent

2019 ◽  
Vol 105 (5) ◽  
pp. 883-893 ◽  
Author(s):  
Xiaowen Tian ◽  
Brian L. Browning ◽  
Sharon R. Browning
Keyword(s):  
Mutation Rate ◽  
Identity By Descent ◽  
Genome Wide

scholarly journals Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass Spectrometry

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Emilia M. Sogin ◽  
Erik Puskás ◽  
Nicole Dubilier ◽  
Manuel Liebeke
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Coral Reef ◽  
Microbial Communities ◽  
Chemical Interaction ◽  
Heterotrophic Bacterium ◽  
Gas Chromatography Mass Spectrometry ◽  
Mangrove Sediment ◽  
Marine Microorganisms ◽  
Marine Habitats

ABSTRACT Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo. First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens. Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans. IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other “omics” (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.

scholarly journals Do Coral Reefs Promote Morphological Diversification? Exploration of Habitat Effects on Labrid Pharyngeal Jaw Evolution in the Era of Big Data

2019 ◽  
Vol 59 (3) ◽  
pp. 696-704 ◽  
Author(s):  
Kory M Evans ◽  
Keiffer L Williams ◽  
Mark W Westneat
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Morphological Evolution ◽  
Morphological Data ◽  
Shape Evolution ◽  
Micro Computed Tomography ◽  
Functional Variation ◽  
Morphological Diversification ◽  
Marine Habitats ◽  
Pharyngeal Jaw

Abstract Coral reefs are complex marine habitats that have been hypothesized to facilitate functional specialization and increased rates of functional and morphological evolution. Wrasses (Labridae: Percomorpha) in particular, have diversified extensively in these coral reef environments and have evolved adaptations to further exploit reef-specific resources. Prior studies have found that reef-dwelling wrasses exhibit higher rates of functional evolution, leading to higher functional variation than in non-reef dwelling wrasses. Here, we examine this hypothesis in the lower pharyngeal tooth plate of 134 species of reef and non-reef-associated labrid fishes using high-resolution morphological data in the form of micro-computed tomography scans and employing three-dimensional geometric morphometrics to quantify shape differences. We find that reef-dwelling wrasses do not differ from non-reef-associated wrasses in morphological disparity or rates of shape evolution. However, we find that some reef-associated species (e.g., parrotfishes and tubelips) exhibit elevated rates of pharyngeal jaw shape evolution and have colonized unique regions of morphospace. These results suggest that while coral reef association may provide the opportunity for specialization and morphological diversification, species must still be able to capitalize on the ecological opportunities to invade novel niche space, and that these novel invasions may prompt rapid rates of morphological evolution in the associated traits that allow them to capitalize on new resources.

pH-mediated control of anti-aggregation activities of cyanobacterial and E. coli chaperonin GroELs

2020 ◽  
Author(s):  
Tahmina Akter ◽  
Hitoshi Nakamoto
Keyword(s):  
Escherichia Coli ◽  
Lactate Dehydrogenase ◽  
Malate Dehydrogenase ◽  
Citrate Synthase ◽  
Ph Dependence ◽  
Chaperone Activity ◽  
Ph Change ◽  
Aggregation Assay ◽  
E Coli ◽  
Aggregation Activity

Abstract In contrast to Escherichia coli, cyanobacteria have multiple GroELs, the bacterial homologues of chaperonin/Hsp60. We have shown that cyanobacterial GroELs are mutually distinct and different from E. coli GroEL with which the paradigm for chaperonin structure/function has been established. However, little is known about regulation of cyanobacterial GroELs. This study investigated effect of pH (varied from 7.0 to 8.5) on chaperone activity of GroEL1 and GroEL2 from the cyanobacterium Synechococcus elongatus PCC7942 and E. coli GroEL. GroEL1 and GroEL2 showed pH dependency in suppression of aggregation of heat-denatured malate dehydrogenase, lactate dehydrogenase and citrate synthase. They exhibited higher anti-aggregation activity at more alkaline pHs. Escherichia coli GroEL showed a similar pH-dependence in suppressing aggregation of heat-denatured lactate dehydrogenase. No pH dependence was observed in all the GroELs when urea-denatured lactate dehydrogenase was used for anti-aggregation assay, suggesting that the pH-dependence is related to some denatured structures. There was no significant influence of pH on the chaperone activity of all the GroELs to promote refolding of heat-denatured malate dehydrogenase. It is known that pH in cyanobacterial cytoplasm increases by one pH unit following a shift from darkness to light, suggesting that the pH-change modulates chaperone activity of cyanobacterial GroEL1 and GroEL2.

scholarly journals The repeatability of genome-wide mutation rate and spectrum estimates

2016 ◽  
Vol 62 (3) ◽  
pp. 507-512 ◽  
Author(s):  
Megan G. Behringer ◽  
David W. Hall
Keyword(s):  
Mutation Rate ◽  
Genome Wide
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